Having the same issue
Word and Excel auto-open when I start up each morning.
There is no checkmark next to "Options > Open at Login" for either program.
There is a checkmark next to "System Preferences > General > Close windows when quitting an application (when selected, open documents and windows will not be restored when you re-open an application)."
There is no other option under "System Preferences > General" related to applications or windows. Similarly, there is no related option appearing under ""System Preferences > Users & Groups > Login Options."
I went to "Finder > Applications > Microsoft Options 2011 > Office > Startup" and found three files in the folder -- for Word, Excel and PowerPoint (which is not auto-opening at startup). I removed those files, and Word and Excel are still auto-opening at startup.
These are all the suggestions I've seen online, and none has made a difference.